void findClosestServer(char **pDb, char **pOrg)
/* If db doesn't have a blat server, look for the closest db (or org) that has one,
* as hgPcr does. */
{
char *db = *pDb, *org = *pOrg;
struct sqlConnection *conn = hConnectCentral();
char query[256];
safef(query, sizeof(query), "select db from blatServers where db = '%s'", db);
if (!sqlExists(conn, query))
{
safef(query, sizeof(query), "select blatServers.db from blatServers,dbDb "
"where blatServers.db = dbDb.name and dbDb.genome = '%s'", org);
char *db = sqlQuickString(conn, query);
if (db == NULL)
{
safef(query, sizeof(query), "select blatServers.db from blatServers,dbDb "
"where blatServers.db = dbDb.name order by dbDb.orderKey,dbDb.name desc");
char *db = sqlQuickString(conn, query);
if (db == NULL)
errAbort("central database tables blatServers and dbDb are disjoint/empty");
else
{
*pDb = db;
*pOrg = hGenome(db);
}
}
else
{
*pDb = db;
*pOrg = hGenome(db);
}
}
hDisconnectCentral(&conn);
}
static unsigned getHubId(char *url, char **errorMessage)
/* find id for url in hubStatus table */
{
struct sqlConnection *conn = hConnectCentral();
char query[4096];
char **row;
boolean foundOne = FALSE;
int id = 0;
char *statusTableName = getHubStatusTableName();
sqlSafef(query, sizeof(query), "select id,errorMessage from %s where hubUrl = \"%s\"", statusTableName, url);
struct sqlResult *sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
if (foundOne)
errAbort("more than one line in %s with hubUrl %s\n",
statusTableName, url);
foundOne = TRUE;
char *thisId = row[0], *thisError = row[1];
if (!isEmpty(thisError))
*errorMessage = cloneString(thisError);
id = sqlUnsigned(thisId);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return id;
}
static void printActiveGenomes()
/* Print out JSON for an object mapping each genome that has at least one db with active=1
* to its taxId. */
{
struct jsonWrite *jw = jsonWriteNew();
jsonWriteObjectStart(jw, NULL);
struct sqlConnection *conn = hConnectCentral();
// Join with defaultDb because in rare cases, different taxIds (species vs. subspecies)
// may be used for different assemblies of the same species. Using defaultDb means that
// we send a taxId consistent with the taxId of the assembly that we'll change to when
// the species is selected from the tree.
char *query = NOSQLINJ "select dbDb.genome, taxId, dbDb.name from dbDb, defaultDb "
"where defaultDb.name = dbDb.name and active = 1 "
"and taxId > 1;"; // filter out experimental hgwdev-only stuff with invalid taxIds
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *genome = row[0], *db = row[2];
int taxId = atoi(row[1]);
if (hDbExists(db))
jsonWriteNumber(jw, genome, taxId);
}
hDisconnectCentral(&conn);
jsonWriteObjectEnd(jw);
puts(jw->dy->string);
jsonWriteFree(&jw);
}
struct pcrServer *getServerList()
/* Get list of available servers. */
{
struct pcrServer *serverList = NULL, *server;
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr;
char **row;
/* Do a little join to get data to fit into the pcrServer. */
sr = sqlGetResult(conn,
"NOSQLINJ select dbDb.name,dbDb.genome,dbDb.description,blatServers.host,"
"blatServers.port,dbDb.nibPath "
"from dbDb,blatServers where "
"dbDb.name = blatServers.db "
"and blatServers.canPcr = 1 order by dbDb.orderKey" );
while ((row = sqlNextRow(sr)) != NULL)
{
AllocVar(server);
server->db = cloneString(row[0]);
server->genome = cloneString(row[1]);
server->description = cloneString(row[2]);
server->host = cloneString(row[3]);
server->port = cloneString(row[4]);
server->seqDir = hReplaceGbdbSeqDir(row[5], server->db);
slAddHead(&serverList, server);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
if (serverList == NULL)
errAbort("Sorry, no PCR servers are available");
slReverse(&serverList);
return serverList;
}
static void disconnectHubsSamePrefix(struct cart *cart, char *url)
/* disconnect all the hubs with the same prefix */
{
char *prefix = cloneString(url);
char *ptr = strrchr(prefix, '/');
if (ptr == NULL)
return;
*ptr = 0;
char query[2048];
sqlSafef(query, sizeof(query), "select id from %s where hubUrl like \"%s%%\"", getHubStatusTableName(), prefix);
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
int id = sqlUnsigned(row[0]);
char buffer[512];
safef(buffer, sizeof(buffer), "hgHubConnect.hub.%d", id);
cartRemove(cart, buffer);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
}
static char *ccFreezeDbConversion(char *database, char *freeze, char *org)
/* Find freeze given database or vice versa. Pass in NULL
* for parameter that is unknown and it will be returned
* as a result. This result can be freeMem'd when done. */
{
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr;
char **row;
char *ret = NULL;
struct dyString *dy = newDyString(128);
if (database != NULL)
dyStringPrintf(dy, "select description from dbDb where name = '%s' and (genome like '%s' or genome like 'Zoo')",
database, org);
else if (freeze != NULL)
dyStringPrintf(dy, "select name from dbDb where description = '%s' and (genome like '%s' or genome like 'Zoo')",
freeze, org);
else
internalErr();
sr = sqlGetResult(conn, dy->string);
if ((row = sqlNextRow(sr)) != NULL)
ret = cloneString(row[0]);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
freeDyString(&dy);
return ret;
}
boolean hubConnectTableExists()
/* Return TRUE if the hubStatus table exists. */
{
struct sqlConnection *conn = hConnectCentral();
boolean exists = sqlTableExists(conn, getHubStatusTableName());
hDisconnectCentral(&conn);
return exists;
}
void checkForGeoMirrorRedirect(struct cart *cart)
// Implement Geo/IP based redirection.
{
char *thisNodeStr = geoMirrorNode();
if (thisNodeStr) // if geo-mirroring is enabled
{
char *redirectCookie = findCookieData("redirect");
char *redirect = cgiOptionalString("redirect");
// if we're not already redirected
if (redirect == NULL && redirectCookie == NULL)
{
int thisNode = sqlUnsigned(thisNodeStr);
struct sqlConnection *centralConn = hConnectCentral();
char *ipStr = cgiRemoteAddr();
int node = defaultNode(centralConn, ipStr);
// if our node is not the node that's closest.
if (thisNode != node)
{
char *geoSuffix = cfgOptionDefault("browser.geoSuffix","");
char query[1056];
sqlSafef(query, sizeof query, "select domain from gbNode%s where node = %d", geoSuffix, node);
char *newDomain = sqlQuickString(centralConn, query);
char *oldDomain = cgiServerName();
char *port = cgiServerPort();
char *uri = cgiRequestUri();
char *sep = strchr(uri, '?') ? "&" : "?";
int newUriSize = strlen(uri) + 1024;
char *newUri = needMem(newUriSize);
char *oldUri = needMem(newUriSize);
safef(oldUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", oldDomain, port, uri, sep, oldDomain);
safef(newUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", newDomain, port, uri, sep, oldDomain);
printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
"<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
"<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
" You might want to navigate to your nearest mirror - %s"
"</h3> "
"<ul style=\"margin:5px;\">",
newDomain);
printf("<li>User settings (sessions and custom tracks) <B>will differ</B> between sites."
"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html#sessions\">Read more.</a></idiv>");
printf("<li>Take me to <a href=\"%s\">%s</a> </li>",
newUri, newDomain);
printf("<li>Let me stay here <a href=\"%s\">%s</a>",
oldUri, oldDomain );
printf("</div></TD></TR>\n");
exit(0);
}
hDisconnectCentral(¢ralConn);
}
}
}
struct serverTable *findServer(char *db, boolean isTrans)
/* Return server for given database. Db can either be
* database name or description. */
{
if (trackHubDatabase(db))
{
struct serverTable *hubSt = trackHubServerTable(db, isTrans);
if (hubSt != NULL)
return hubSt;
errAbort("Cannot get blat server parameters for track hub with database %s\n", db);
}
static struct serverTable st;
struct sqlConnection *conn = hConnectCentral();
char query[256];
struct sqlResult *sr;
char **row;
char dbActualName[32];
/* If necessary convert database description to name. */
sqlSafef(query, sizeof(query), "select name from dbDb where name = '%s'", db);
if (!sqlExists(conn, query))
{
sqlSafef(query, sizeof(query), "select name from dbDb where description = '%s'", db);
if (sqlQuickQuery(conn, query, dbActualName, sizeof(dbActualName)) != NULL)
db = dbActualName;
}
/* Do a little join to get data to fit into the serverTable. */
sqlSafef(query, sizeof(query), "select dbDb.name,dbDb.description,blatServers.isTrans"
",blatServers.host,blatServers.port,dbDb.nibPath "
"from dbDb,blatServers where blatServers.isTrans = %d and "
"dbDb.name = '%s' and dbDb.name = blatServers.db",
isTrans, db);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
{
errAbort("Can't find a server for %s database %s. Click "
"<A HREF=\"/cgi-bin/hgBlat?%s&command=start&db=%s\">here</A> "
"to reset to default database.",
(isTrans ? "translated" : "DNA"), db,
cartSidUrlString(cart), hDefaultDb());
}
st.db = cloneString(row[0]);
st.genome = cloneString(row[1]);
st.isTrans = atoi(row[2]);
st.host = cloneString(row[3]);
st.port = cloneString(row[4]);
st.nibDir = hReplaceGbdbSeqDir(row[5], st.db);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return &st;
}
char *hubNameFromUrl(char *hubUrl)
/* Given the URL for a hub, return its hub_# name. */
{
char query[PATH_LEN*4];
sqlSafef(query, sizeof(query), "select concat('hub_', id) from %s where hubUrl = '%s'",
getHubStatusTableName(), hubUrl);
struct sqlConnection *conn = hConnectCentral();
char *name = sqlQuickString(conn, query);
hDisconnectCentral(&conn);
return name;
}
int searchProteinsInSupportedGenomes(char *queryID, char **database)
/* search existing genome databases to see if they contain the protein
Input: queryID
return: number of proteins found in existing genome databases
output: the last genome database is stored at *database
*/
{
int pbProteinCnt = {0};
char *gDatabase;
char *org = NULL;
char cond_str[255];
struct sqlConnection *conn;
struct sqlConnection *connCentral;
char queryCentral[256];
struct sqlResult *srCentral;
char **row3;
char *answer;
/* get all genome DBs that support PB */
connCentral = hConnectCentral();
sqlSafef(queryCentral, sizeof(queryCentral),
"select defaultDb.name, dbDb.organism from dbDb,defaultDb where hgPbOk=1 and defaultDb.name=dbDb.name");
srCentral = sqlMustGetResult(connCentral, queryCentral);
row3 = sqlNextRow(srCentral);
/* go through each valid genome database that has PB */
while (row3 != NULL)
{
gDatabase = row3[0];
org = row3[1];
conn = sqlConnect(gDatabase);
sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s'", queryID);
answer = sqlGetField(gDatabase, "kgSpAlias", "count(distinct spID)", cond_str);
sqlDisconnect(&conn);
if ((answer != NULL) && (!sameWord(answer, "0")))
{
/* increase the count only by one, because new addition of splice variants to kgSpAlias
would give a count of 2 for both the parent and the variant, which caused the
problem when rescale button is pressed */
if (atoi(answer) > 0) pbProteinCnt++;
*database = strdup(gDatabase);
}
row3 = sqlNextRow(srCentral);
}
sqlFreeResult(&srCentral);
hDisconnectCentral(&connCentral);
return(pbProteinCnt);
}
struct hubConnectStatus *hubFromId(unsigned hubId)
/* Given a hub ID number, return corresponding trackHub structure.
* ErrAbort if there's a problem. */
{
struct sqlConnection *conn = hConnectCentral();
struct hubConnectStatus *status = hubConnectStatusForId(conn, hubId);
hDisconnectCentral(&conn);
if (status == NULL)
errAbort("The hubId %d was not found", hubId);
if (!isEmpty(status->errorMessage))
errAbort("%s", status->errorMessage);
return status;
}
char *hDbOrganism(char *database)
/* Function to get organism from the genome db */
{
struct sqlConnection *connCentral = hConnectCentral();
char buf[128];
char query[256];
char *res;
sqlSafef(query, sizeof(query), "select organism from dbDb where name = '%s'",
database);
res = strdup(sqlQuickQuery(connCentral, query, buf, sizeof(buf)));
hDisconnectCentral(&connCentral);
return res;
}
static void insertHubUrlInStatus(char *url)
/* add a url to the hubStatus table */
{
struct sqlConnection *conn = hConnectCentral();
char query[4096];
char *statusTable = getHubStatusTableName();
if (sqlFieldIndex(conn, statusTable, "firstAdded") >= 0)
sqlSafef(query, sizeof(query), "insert into %s (hubUrl,firstAdded) values (\"%s\",now())",
statusTable, url);
else
sqlSafef(query, sizeof(query), "insert into %s (hubUrl) values (\"%s\")",
statusTable, url);
sqlUpdate(conn, query);
hDisconnectCentral(&conn);
}
struct hash *hgHubConnectPublic()
/* Put up the list of public hubs and other controls for the page. */
{
struct hash *retHash = NULL;
struct sqlConnection *conn = hConnectCentral();
char *publicTable = cfgOptionEnvDefault("HGDB_HUB_PUBLIC_TABLE",
hubPublicTableConfVariable, defaultHubPublicTableName);
if (!(sqlTableExists(conn, publicTable) &&
(retHash = outputPublicTable(conn, publicTable)) != NULL ))
{
printf("<div id=\"publicHubs\" class=\"hubList\"> \n");
printf("No Public Track Hubs for this genome assembly<BR>");
printf("</div>");
}
hDisconnectCentral(&conn);
return retHash;
}
static char *genomeDbForImage(struct sqlConnection *conn, int imageId)
/* Return the genome database to associate with image or NULL if none. */
{
char *db;
char *scientificName = visiGeneOrganism(conn, imageId);
struct sqlConnection *cConn = hConnectCentral();
char query[256];
safef(query, sizeof(query),
"select defaultDb.name from defaultDb,dbDb where "
"defaultDb.genome = dbDb.organism and "
"dbDb.active = 1 and "
"dbDb.scientificName = '%s'"
, scientificName);
db = sqlQuickString(cConn, query);
hDisconnectCentral(&cConn);
return db;
}
static void tryHubOpen(unsigned id)
/* try to open hub, leaks trackHub structure */
{
/* try opening this again to reset error */
struct sqlConnection *conn = hConnectCentral();
struct errCatch *errCatch = errCatchNew();
struct hubConnectStatus *hub = NULL;
if (errCatchStart(errCatch))
hub = hubConnectStatusForId(conn, id);
errCatchEnd(errCatch);
if (errCatch->gotError)
hubUpdateStatus( errCatch->message->string, NULL);
else
hubUpdateStatus(NULL, hub);
errCatchFree(&errCatch);
hDisconnectCentral(&conn);
}
static struct aHubMatch *filterTrixSearchMatches(struct dbDb *dbDbList,
struct trixSearchResult *tsrList)
/* Collect the assembly hub matches (not track hub matches) from a search in hub trix files. */
{
if (tsrList == NULL)
return NULL;
struct aHubMatch *aHubMatchList = NULL;
// Make a hash of local dbs so we can tell which hub dbs must be assembly hubs
// not track hubs.
struct hash *localDbs = hashNew(0);
struct dbDb *dbDb;
for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next)
hashStore(localDbs, dbDb->name);
// tsrList gives hub URLs which we can then look up in hubPublic.
struct dyString *query = sqlDyStringCreate("select shortLabel,hubUrl,dbList from %s "
"where hubUrl in (",
hubPublicTableName());
struct trixSearchResult *tsr;
for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
{
if (tsr != tsrList)
dyStringAppend(query, ", ");
dyStringPrintf(query, "'%s'", tsr->itemId);
}
dyStringAppendC(query, ')');
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr = sqlGetResult(conn, query->string);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *shortLabel = row[0];
char *hubUrl = row[1];
struct slName *dbName, *dbList = slNameListFromComma(row[2]);
for (dbName = dbList; dbName != NULL; dbName = dbName->next)
if (! hashLookup(localDbs, dbName->name))
{
slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name));
}
}
slReverse(&aHubMatchList);
hDisconnectCentral(&conn);
return aHubMatchList;
}
void printCladeListHtml(char *genome, char *onChangeText)
/* Make an HTML select input listing the clades. */
{
char **row = NULL;
char *clades[128];
char *labels[128];
char *defaultClade = hClade(genome);
char *defaultLabel = NULL;
int numClades = 0;
struct sqlConnection *conn = hConnectCentral(); // after hClade since it access hgcentral too
// get only the clades that have actual active genomes
char query[4096];
safef(query, sizeof query, "NOSQLINJ SELECT DISTINCT(c.name), c.label FROM %s c, %s g, %s d WHERE c.name=g.clade AND d.organism=g.genome AND d.active=1 ORDER BY c.priority", cladeTable(),genomeCladeTable(), dbDbTable());
struct sqlResult *sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
clades[numClades] = cloneString(row[0]);
labels[numClades] = cloneString(row[1]);
if (sameWord(defaultClade, clades[numClades]))
defaultLabel = clades[numClades];
numClades++;
if (numClades >= ArraySize(clades))
internalErr();
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
struct slPair *names = trackHubGetCladeLabels();
for(; names; names = names->next)
{
clades[numClades] = names->name;
labels[numClades] = names->val;
if (sameWord(defaultClade, clades[numClades]))
defaultLabel = clades[numClades];
numClades++;
if (numClades >= ArraySize(clades))
internalErr();
}
cgiMakeDropListFull(cladeCgiName, labels, clades, numClades,
defaultLabel, onChangeText);
}
void getChromNamesAndDirForDb(char *db)
{
struct sqlConnection *conn = hConnectCentral();
char query[512];
char buff[512];
char *tmpMark = NULL;
int buffSize = 512;
sqlSafef(query, sizeof(query), "select nibPath from dbDb where name='%s'", db);
if(sqlQuickQuery(conn, query, buff, buffSize) == NULL)
errAbort("Coun't find nib dir for genome %s\n", db);
dirName = needMem(buffSize*sizeof(char));
tmpMark = strrchr(buff, '/');
if(tmpMark != NULL)
*tmpMark = '\0';
snprintf(dirName, buffSize, "%s/mixedNib/", buff);
chromNames = hAllChromNames();
hDisconnectCentral(&conn);
}
unsigned hubClearStatus(char *url)
/* drop the information about this url from the hubStatus table */
{
struct sqlConnection *conn = hConnectCentral();
char query[512];
sqlSafef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", getHubStatusTableName(), url);
unsigned id = sqlQuickNum(conn, query);
if (id == 0)
errAbort("could not find url %s in status table (%s)\n",
url, getHubStatusTableName());
sqlSafef(query, sizeof(query), "delete from %s where hubUrl = \"%s\"", getHubStatusTableName(), url);
sqlUpdate(conn, query);
hDisconnectCentral(&conn);
return id;
}
struct hubConnectStatus *hubConnectStatusListFromCartAll(struct cart *cart)
/* Return list of all track hubs that are referenced by cart. */
{
struct hubConnectStatus *hubList = NULL, *hub;
struct slPair *pair, *pairList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
struct sqlConnection *conn = hConnectCentral();
for (pair = pairList; pair != NULL; pair = pair->next)
{
int id = hubIdFromCartName(pair->name);
hub = hubConnectStatusForId(conn, id);
if (hub != NULL)
{
slAddHead(&hubList, hub);
}
}
slFreeList(&pairList);
hDisconnectCentral(&conn);
slReverse(&hubList);
return hubList;
}
struct hubConnectStatus *hubConnectStatusListFromCart(struct cart *cart)
/* Return list of track hubs that are turned on by user in cart. */
{
struct hubConnectStatus *hubList = NULL, *hub;
struct slName *name, *nameList = hubConnectHubsInCart(cart);
struct sqlConnection *conn = hConnectCentral();
for (name = nameList; name != NULL; name = name->next)
{
int id = sqlSigned(name->name);
hub = hubConnectStatusForId(conn, id);
if (hub != NULL)
{
slAddHead(&hubList, hub);
}
}
slFreeList(&nameList);
hDisconnectCentral(&conn);
slReverse(&hubList);
return hubList;
}
unsigned hubResetError(char *url)
/* clear the error for this url in the hubStatus table,return the id */
{
struct sqlConnection *conn = hConnectCentral();
char query[512];
sqlSafef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", getHubStatusTableName(), url);
unsigned id = sqlQuickNum(conn, query);
if (id == 0)
errAbort("could not find url %s in status table (%s)\n",
url, getHubStatusTableName());
sqlSafef(query, sizeof(query), "update %s set errorMessage=\"\" where hubUrl = \"%s\"", getHubStatusTableName(), url);
sqlUpdate(conn, query);
hDisconnectCentral(&conn);
return id;
}
struct targetPcrServer *getTargetServerList(char *db, char *name)
/* Get list of available non-genomic-assembly target pcr servers associated
* with db (and name, if not NULL). There may be none -- that's fine. */
{
struct targetPcrServer *serverList = NULL, *server;
struct sqlConnection *conn = hConnectCentral();
struct sqlConnection *conn2 = hAllocConn(db);
struct sqlResult *sr;
char **row;
struct dyString *dy = dyStringNew(0);
sqlDyStringPrintf(dy,
"select b.host, b.port, t.* from targetDb as t, blatServers as b "
"where b.db = t.name and t.db = '%s' and b.canPcr = 1 ",
db);
if (isNotEmpty(name))
sqlDyStringPrintf(dy, "and t.name = '%s' ", name);
dyStringAppend(dy, "order by t.priority");
sr = sqlGetResult(conn, dy->string);
while ((row = sqlNextRow(sr)) != NULL)
{
/* Keep this server only if its timestamp is newer than the tables
* and file on which it depends. */
struct targetDb *target = targetDbMaybeLoad(conn2, row+2);
if (target != NULL)
{
AllocVar(server);
server->host = cloneString(row[0]);
server->port = cloneString(row[1]);
server->targetDb = target;
slAddHead(&serverList, server);
}
}
dyStringFree(&dy);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
hFreeConn(&conn2);
slReverse(&serverList);
return serverList;
}
void hubUpdateStatus(char *errorMessage, struct hubConnectStatus *hub)
/* set the error message in the hubStatus table */
{
struct sqlConnection *conn = hConnectCentral();
char query[64 * 1024];
struct trackHub *tHub = NULL;
if (hub != NULL)
tHub = hub->trackHub;
if (errorMessage != NULL)
{
// make sure there is no newline at the end. This should be unneccesary
// but there are many, many places where newlines are added in calls
// to warn and errAbort
char buffer[64 * 1024];
safecpy(buffer, sizeof buffer, errorMessage);
while (lastChar(buffer) == '\n')
buffer[strlen(buffer) - 1] = '\0';
sqlSafef(query, sizeof(query),
"update %s set errorMessage=\"%s\", lastNotOkTime=now() where id=%d",
getHubStatusTableName(), buffer, hub->id);
sqlUpdate(conn, query);
}
else if (tHub != NULL)
{
int dbCount = 0;
char *dbList = getDbList(tHub, &dbCount);
// users may include quotes in their hub names requiring escaping
sqlSafef(query, sizeof(query),
"update %s set shortLabel=\"%s\",longLabel=\"%s\",dbCount=\"%d\",dbList=\"%s\",errorMessage=\"\",lastOkTime=now() where id=%d",
getHubStatusTableName(), tHub->shortLabel, tHub->longLabel,
dbCount, dbList,
hub->id);
sqlUpdate(conn, query);
}
hDisconnectCentral(&conn);
}
struct dbDb *loadDbInformation_mod(char *database)
/* load up the information for a particular draft */
{
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr = NULL;
char **row;
struct dbDb *dbList = NULL, *db = NULL;
char query[256];
snprintf(query, sizeof(query), "select * from dbDb where name='%s'", database);
/* Scan through dbDb table, loading into list */
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
db = dbDbLoad(row);
slAddHead(&dbList, db);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
if(slCount(dbList) != 1)
errAbort("coordConv.c::loadDbInformation() - expecting 1 dbDb record for %s got %d", db, slCount(dbList));
return dbList;
}
struct galleryEntry *galleryFetch()
/* Return an slList of gallery entries fetched from hgcentral */
{
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr = NULL;
struct galleryEntry *gal, *galList = NULL;
char otherConstraints[80] = "", query[2048], **row;
sqlSafef (query, sizeof(query),
"select m.realName, s.userName, m.idx, s.sessionName, s.useCount, s.settings, s.contents, s.firstUse from "
"%s s left join gbMembers m on m.userName = s.userName where shared = 2%s limit 30"
, namedSessionTable, otherConstraints);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
gal = galLoad(row);
slAddHead (&galList, gal);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return galList;
}
void makeActiveImagePB(char *psOutput, char *psOutput2)
/* Make image and image map. */
{
char *mapName = "map";
int pixWidth, pixHeight;
char *answer;
char cond_str[255];
struct sqlConnection *conn;
struct sqlConnection *connCentral;
char query[256];
struct sqlResult *sr;
char **row;
int iypos;
char *blatGbDb;
char *sciName, *commonName;
char *spDisplayId;
char *oldDisplayId;
conn = sqlConnect(UNIPROT_DB_NAME);
hPrintf("<br><font size=4>Protein ");
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" TARGET=_blank><B>%s</B></A>\n",
proteinID, proteinID);
spDisplayId = spAccToId(conn, spFindAcc(conn, proteinID));
if (strstr(spDisplayId, spFindAcc(conn, proteinID)) == NULL)
{
hPrintf(" (aka %s", spDisplayId);
/* show once if the new and old displayId are the same */
oldDisplayId = oldSpDisplayId(spDisplayId);
if (oldDisplayId != NULL)
{
if (!sameWord(spDisplayId, oldDisplayId))
{
hPrintf(" or %s", oldSpDisplayId(spDisplayId));
}
}
hPrintf(")\n");
}
hPrintf(" %s\n", description);
hPrintf("</font><br>");
hPrintf("Organism: ");
/* get scientific and Genbank common name of this organism */
sciName = NULL;
commonName = NULL;
sqlSafefFrag(cond_str, sizeof(cond_str),"accession='%s'", proteinID);
answer = sqlGetField(PROTEOME_DB_NAME, "spXref3", "division", cond_str);
if (answer != NULL)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='scientific name'", answer);
sciName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='genbank common name'", answer);
commonName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
}
if (sciName != NULL)
{
hPrintf("%s", sciName);
}
if (commonName != NULL)
{
hPrintf(" (%s)", commonName);
}
hPrintf("<br>");
protSeq = getAA(proteinID);
if (protSeq == NULL)
{
hUserAbort("%s is not a current valid entry in UniProtKB\n", proteinID);
}
protSeqLen = strlen(protSeq);
fflush(stdout);
iypos = 15;
doTracks(proteinID, mrnaID, protSeq, &iypos, psOutput);
if (!hTableExists(database, "pbStamp")) goto histDone;
pbScale = 3;
pixWidth = 765;
insideWidth = pixWidth-gfxBorder;
pixHeight = 350;
if (psOutput2)
{
vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2);
}
else
{
trashDirFile(&gifTn2, "pbt", "pbt", ".png");
vg2 = vgOpenPng(pixWidth, pixHeight, gifTn2.forCgi, FALSE);
}
g_vg = vg2;
pbRed = vgFindColorIx(vg2, 0xf9, 0x51, 0x59);
pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);
normalColor = pbBlue;
abnormalColor = pbRed;
bkgColor = vgFindColorIx(vg2, 255, 254, 232);
vgBox(vg2, 0, 0, insideWidth, pixHeight, bkgColor);
/* Start up client side map. */
mapName=cloneString("pbStamps");
hPrintf("\n<MAP Name=%s>\n", mapName);
vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
iypos = 15;
/* Draw stamps. */
doStamps(proteinID, mrnaID, protSeq, vg2, &iypos);
/* Finish map. */
hPrintf("</MAP>\n");
/* Save out picture and tell html file about it. */
vgClose(&vg2);
hPrintf("<P>");
hPrintf("\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
gifTn2.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
{
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
}
else
{
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
}
hPrintf("Explanation of Protein Property Histograms</A><BR>");
hPrintf("<P>");
histDone:
hPrintf("<P>");
fflush(stdout);
/* See if a UCSC Genome Browser exist for this organism. If so, display BLAT link. */
connCentral = hConnectCentral();
sqlSafef(query, sizeof(query),
"select defaultDb.name from dbDb, defaultDb where dbDb.scientificName='%s' and dbDb.name=defaultDb.name",
sciName);
sr = sqlGetResult(connCentral, query);
row = sqlNextRow(sr);
if (row != NULL)
{
blatGbDb = strdup(row[0]);
}
else
{
blatGbDb = NULL;
}
sqlFreeResult(&sr);
hDisconnectCentral(&connCentral);
if (proteinInSupportedGenome || (blatGbDb != NULL))
{
hPrintf("\n<B>UCSC Links:</B><BR>\n ");
hPrintf("<UL>\n");
/* Show GB links only if the protein belongs to a supported genome */
if (proteinInSupportedGenome)
{
doGenomeBrowserLink(proteinID, mrnaID, hgsidStr);
doGeneDetailsLink(proteinID, mrnaID, hgsidStr);
}
/* Show Gene Sorter link only if it is valid for this genome */
if (hgNearOk(database))
{
doGeneSorterLink(protDisplayID, mrnaID, hgsidStr);
}
/* Show BLAT link if we have UCSC Genome Browser for it */
if (blatGbDb != NULL)
{
doBlatLink(blatGbDb, sciName, commonName, protSeq);
}
hPrintf("</UL><P>");
}
/* This section shows various types of domains */
conn = sqlConnect(UNIPROT_DB_NAME);
domainsPrint(conn, proteinID);
hPrintf("<P>");
/* Do Pathway section only if the protein belongs to a supported genome */
if (proteinInSupportedGenome);
{
doPathwayLinks(proteinID, mrnaID);
}
printFASTA(proteinID, protSeq);
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display. */
{
struct sqlConnection *conn, *conn2;
struct sqlConnection *connCentral = hConnectCentral();
char query[256], query2[256];
struct sqlResult *sr, *sr2;
char **row, **row2;
char buf[128];
char *answer;
char *database;
char *genome, *genomeDesc;
char *kgID, *chrom, *txStart, *txEnd;
int iCnt = 1;
cart = theCart;
cartWebStart(theCart, database, "UCSC Known Genes List \n");
getDbAndGenome(cart, &database, &genome, oldVars);
if (!hTableExistsDb(database, "knownGene"))
{
printf("<br>Database %s currently does not have UCSC Known Genes.", database);
cartWebEnd();
return;
}
sprintf(query, "select description from dbDb where name = '%s'", database);
genomeDesc = strdup(sqlQuickQuery(connCentral, query, buf, sizeof(buf)));
hDisconnectCentral(&connCentral);
printf("<H2>%s Genome (%s Assembly)</H2>\n", genome, genomeDesc);
conn = hAllocConn(database);
conn2= hAllocConn(database);
sprintf(query2,"select kgID from %s.kgXref order by geneSymbol;",
database);
/* use the following for quck testing */
/*sprintf(query2,"select kgID, geneSymbol, description, spID, refseq from %s.kgXref order by geneSymbol limit 10;", database);
*/
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
kgID = row2[0];
sprintf(query,"select chrom, txSTart, txEnd from %s.knownGene where name='%s'", database, kgID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
chrom = row[0];
txStart = row[1];
txEnd = row[2];
printf("<A href=\"/cgi-bin/hgGene?db=%s&hgg_gene=%s",
database, kgID);
printf("&hgg_chrom=%s&hgg_start=%s&hgg_end=%s\">", chrom, txStart, txEnd);
printf("%d</A><BR>\n", iCnt);
iCnt++;
if ((iCnt % 1000) == 0) fflush(stdout);
sqlFreeResult(&sr);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
cartWebEnd();
}
